Multiple sequence alignment - TraesCS5B01G137600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G137600 chr5B 100.000 4226 0 0 1 4226 259537082 259541307 0.000000e+00 7805.0
1 TraesCS5B01G137600 chr5B 95.918 49 1 1 289 337 259537340 259537387 1.260000e-10 78.7
2 TraesCS5B01G137600 chr5B 95.918 49 1 1 259 306 259537370 259537418 1.260000e-10 78.7
3 TraesCS5B01G137600 chr5D 95.255 2466 92 16 289 2736 242355906 242358364 0.000000e+00 3882.0
4 TraesCS5B01G137600 chr5D 91.661 1487 83 17 2751 4226 242358352 242359808 0.000000e+00 2021.0
5 TraesCS5B01G137600 chr5D 91.830 306 25 0 1 306 242355648 242355953 1.090000e-115 427.0
6 TraesCS5B01G137600 chr5A 93.471 2466 110 28 289 2737 310875791 310873360 0.000000e+00 3615.0
7 TraesCS5B01G137600 chr5A 92.220 1491 79 17 2751 4226 310873373 310871905 0.000000e+00 2076.0
8 TraesCS5B01G137600 chr4D 88.053 837 93 6 1183 2016 109911952 109911120 0.000000e+00 985.0
9 TraesCS5B01G137600 chr4D 83.071 254 28 9 406 645 416060712 416060964 2.560000e-52 217.0
10 TraesCS5B01G137600 chr4A 87.694 837 96 6 1183 2016 466926025 466926857 0.000000e+00 968.0
11 TraesCS5B01G137600 chr4A 81.600 250 34 9 406 645 47751185 47750938 3.330000e-46 196.0
12 TraesCS5B01G137600 chr4B 86.619 837 105 6 1183 2016 171028540 171027708 0.000000e+00 918.0
13 TraesCS5B01G137600 chr1A 81.220 836 145 12 1183 2012 500343352 500342523 0.000000e+00 664.0
14 TraesCS5B01G137600 chr1D 81.064 808 141 12 1211 2012 404970783 404969982 5.960000e-178 634.0
15 TraesCS5B01G137600 chr3A 82.674 531 88 4 1183 1711 579552998 579553526 6.400000e-128 468.0
16 TraesCS5B01G137600 chr3A 83.648 159 26 0 403 561 523751868 523751710 2.630000e-32 150.0
17 TraesCS5B01G137600 chr3A 90.000 60 5 1 2335 2394 467018983 467019041 4.530000e-10 76.8
18 TraesCS5B01G137600 chr3D 82.298 531 90 4 1183 1711 439838745 439839273 1.380000e-124 457.0
19 TraesCS5B01G137600 chr3D 80.800 250 32 11 407 642 590409481 590409728 9.330000e-42 182.0
20 TraesCS5B01G137600 chr3D 80.816 245 34 8 403 644 579587103 579586869 3.360000e-41 180.0
21 TraesCS5B01G137600 chr3D 75.000 244 42 14 410 645 606073184 606072952 1.250000e-15 95.3
22 TraesCS5B01G137600 chr6B 79.599 299 55 5 1668 1963 717076324 717076029 4.280000e-50 209.0
23 TraesCS5B01G137600 chr6A 78.261 299 59 5 1668 1963 617657602 617657897 2.010000e-43 187.0
24 TraesCS5B01G137600 chr3B 86.066 122 17 0 403 524 816009401 816009280 9.530000e-27 132.0
25 TraesCS5B01G137600 chr2B 77.533 227 37 9 413 626 100030865 100031090 1.600000e-24 124.0
26 TraesCS5B01G137600 chr7D 90.909 55 5 0 2335 2389 622401682 622401628 1.630000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G137600 chr5B 259537082 259541307 4225 False 2654.133333 7805 97.278667 1 4226 3 chr5B.!!$F1 4225
1 TraesCS5B01G137600 chr5D 242355648 242359808 4160 False 2110.000000 3882 92.915333 1 4226 3 chr5D.!!$F1 4225
2 TraesCS5B01G137600 chr5A 310871905 310875791 3886 True 2845.500000 3615 92.845500 289 4226 2 chr5A.!!$R1 3937
3 TraesCS5B01G137600 chr4D 109911120 109911952 832 True 985.000000 985 88.053000 1183 2016 1 chr4D.!!$R1 833
4 TraesCS5B01G137600 chr4A 466926025 466926857 832 False 968.000000 968 87.694000 1183 2016 1 chr4A.!!$F1 833
5 TraesCS5B01G137600 chr4B 171027708 171028540 832 True 918.000000 918 86.619000 1183 2016 1 chr4B.!!$R1 833
6 TraesCS5B01G137600 chr1A 500342523 500343352 829 True 664.000000 664 81.220000 1183 2012 1 chr1A.!!$R1 829
7 TraesCS5B01G137600 chr1D 404969982 404970783 801 True 634.000000 634 81.064000 1211 2012 1 chr1D.!!$R1 801
8 TraesCS5B01G137600 chr3A 579552998 579553526 528 False 468.000000 468 82.674000 1183 1711 1 chr3A.!!$F2 528
9 TraesCS5B01G137600 chr3D 439838745 439839273 528 False 457.000000 457 82.298000 1183 1711 1 chr3D.!!$F1 528

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
180 181 0.040958 GACCGTGACACGTCGTAGTT 60.041 55.000 25.18 1.83 40.58 2.24 F
1257 1272 1.065273 GACGTACACCATCGGCGAT 59.935 57.895 18.14 18.14 0.00 4.58 F
2459 2477 0.741915 GGGCAACAAGTTTTCGGACA 59.258 50.000 0.00 0.00 39.74 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1935 1950 0.620556 TCCTGACAAGATCCTTGGCC 59.379 55.0 9.77 0.0 0.00 5.36 R
3144 3170 0.179111 TCATCATCGCCACGAACTCC 60.179 55.0 0.00 0.0 39.99 3.85 R
4149 4205 0.035820 TATCCGCCACCACCTGTTTC 60.036 55.0 0.00 0.0 0.00 2.78 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.731819 ACTCGTTAGTACAACACAAGATATATG 57.268 33.333 0.00 0.00 32.84 1.78
65 66 1.153168 CATTGTAGCACCTCCCCCG 60.153 63.158 0.00 0.00 0.00 5.73
69 70 2.363795 TAGCACCTCCCCCGTCTG 60.364 66.667 0.00 0.00 0.00 3.51
81 82 2.125106 CGTCTGCCCAACCTAGCC 60.125 66.667 0.00 0.00 0.00 3.93
118 119 7.291566 ACTAGTGCACCTTCTACTATAGTCAT 58.708 38.462 14.63 0.00 0.00 3.06
123 124 7.928706 GTGCACCTTCTACTATAGTCATCATTT 59.071 37.037 9.12 0.00 0.00 2.32
126 127 9.186323 CACCTTCTACTATAGTCATCATTTTCG 57.814 37.037 9.12 0.00 0.00 3.46
128 129 9.751542 CCTTCTACTATAGTCATCATTTTCGTT 57.248 33.333 9.12 0.00 0.00 3.85
130 131 9.447040 TTCTACTATAGTCATCATTTTCGTTCG 57.553 33.333 9.12 0.00 0.00 3.95
131 132 8.618677 TCTACTATAGTCATCATTTTCGTTCGT 58.381 33.333 9.12 0.00 0.00 3.85
160 161 4.344968 CCACATCTACACTCACATCCCATA 59.655 45.833 0.00 0.00 0.00 2.74
164 165 4.215908 TCTACACTCACATCCCATAGACC 58.784 47.826 0.00 0.00 0.00 3.85
180 181 0.040958 GACCGTGACACGTCGTAGTT 60.041 55.000 25.18 1.83 40.58 2.24
192 193 4.790140 CACGTCGTAGTTTATTAACGAGCT 59.210 41.667 0.00 0.00 45.35 4.09
209 210 1.310933 GCTCTTGTGGGTGCTCATGG 61.311 60.000 0.00 0.00 0.00 3.66
266 267 8.922058 CAGATTTTCTGCATGTTAAGCTTAAT 57.078 30.769 21.28 4.36 37.72 1.40
267 268 8.804743 CAGATTTTCTGCATGTTAAGCTTAATG 58.195 33.333 21.28 16.84 37.72 1.90
268 269 8.742777 AGATTTTCTGCATGTTAAGCTTAATGA 58.257 29.630 21.28 11.94 0.00 2.57
269 270 8.922058 ATTTTCTGCATGTTAAGCTTAATGAG 57.078 30.769 21.28 14.30 0.00 2.90
354 355 4.642429 CTGAGTAGCTTGTTAAACCACCT 58.358 43.478 0.00 0.00 0.00 4.00
398 399 2.417787 CCACTACAGCGGTTAAGGTACC 60.418 54.545 2.73 2.73 34.72 3.34
411 412 5.379187 GTTAAGGTACCTGTTCCCTTTCAA 58.621 41.667 17.14 0.00 39.30 2.69
429 430 9.284968 CCCTTTCAAAATATAAGGTGTATCGAT 57.715 33.333 2.16 2.16 37.35 3.59
465 467 7.800155 TCAAACTTGTGTATGTTTGATCAGA 57.200 32.000 14.65 0.00 46.88 3.27
542 545 5.786401 ACTTTCTGTGATGAATCTAACGC 57.214 39.130 0.00 0.00 0.00 4.84
558 561 9.821662 GAATCTAACGCTACAAATTTGTTACTT 57.178 29.630 27.66 15.83 42.35 2.24
702 707 4.838486 GACGGCTCAGCGACGAGG 62.838 72.222 0.00 0.00 33.36 4.63
708 713 2.033602 TCAGCGACGAGGTCAGGA 59.966 61.111 0.00 0.00 32.09 3.86
752 757 1.400142 TCCAATCAAAGCGGTATTGCG 59.600 47.619 3.57 0.00 40.67 4.85
755 760 1.299541 ATCAAAGCGGTATTGCGAGG 58.700 50.000 0.00 0.00 40.67 4.63
766 771 2.401583 ATTGCGAGGAATGCTACACA 57.598 45.000 0.00 0.00 0.00 3.72
850 859 1.303236 CGCCATTCACTCCCAACCA 60.303 57.895 0.00 0.00 0.00 3.67
925 934 4.474198 AACTTTGGTTTGTGCATGTGTGC 61.474 43.478 0.00 0.00 41.29 4.57
948 957 2.002586 GTGCGTACTCTTCATGCATGT 58.997 47.619 25.43 9.20 39.91 3.21
1257 1272 1.065273 GACGTACACCATCGGCGAT 59.935 57.895 18.14 18.14 0.00 4.58
1620 1635 2.436646 GTGATGCACCGGGACCTG 60.437 66.667 6.32 0.00 0.00 4.00
1839 1854 4.689549 TTCCTCTCCGGCGTCCCA 62.690 66.667 6.01 0.00 0.00 4.37
1935 1950 3.809013 CCCAACATCTCCCCCGGG 61.809 72.222 15.80 15.80 0.00 5.73
1965 1980 2.639347 TCTTGTCAGGAAGATGCTCCAA 59.361 45.455 0.00 0.00 38.02 3.53
1980 1995 2.889756 GCTCCAAATCAACCCCAAGGAT 60.890 50.000 0.00 0.00 36.73 3.24
2017 2032 3.070018 CAAGTCCTCAGTAAGCCACTTG 58.930 50.000 0.00 0.00 37.71 3.16
2049 2064 4.908601 TTTTTCCTCCTGTCAGATGCTA 57.091 40.909 0.00 0.00 0.00 3.49
2065 2080 1.417592 CTAGCTTCGTGCACGCTTG 59.582 57.895 33.63 24.13 45.94 4.01
2067 2082 1.282248 TAGCTTCGTGCACGCTTGTC 61.282 55.000 33.63 19.01 45.94 3.18
2080 2097 1.838345 CGCTTGTCGTACTACATGACG 59.162 52.381 15.11 13.37 44.85 4.35
2259 2276 3.774766 AGTAGGCACATGGACTGACATTA 59.225 43.478 0.00 0.00 33.87 1.90
2265 2282 4.711721 CACATGGACTGACATTAACAACG 58.288 43.478 0.00 0.00 0.00 4.10
2459 2477 0.741915 GGGCAACAAGTTTTCGGACA 59.258 50.000 0.00 0.00 39.74 4.02
2712 2738 3.945640 AGGACAACAGTGGGTAAGTTT 57.054 42.857 0.00 0.00 0.00 2.66
2713 2739 5.127491 CAAGGACAACAGTGGGTAAGTTTA 58.873 41.667 0.00 0.00 0.00 2.01
2737 2763 5.954335 AGCACCAACAAACTGATAATTAGC 58.046 37.500 0.00 0.00 0.00 3.09
2738 2764 5.102313 GCACCAACAAACTGATAATTAGCC 58.898 41.667 0.00 0.00 0.00 3.93
2739 2765 5.650543 CACCAACAAACTGATAATTAGCCC 58.349 41.667 0.00 0.00 0.00 5.19
2740 2766 4.398044 ACCAACAAACTGATAATTAGCCCG 59.602 41.667 0.00 0.00 0.00 6.13
2741 2767 4.351192 CAACAAACTGATAATTAGCCCGC 58.649 43.478 0.00 0.00 0.00 6.13
2743 2769 4.013728 ACAAACTGATAATTAGCCCGCAA 58.986 39.130 0.00 0.00 0.00 4.85
2744 2770 4.461081 ACAAACTGATAATTAGCCCGCAAA 59.539 37.500 0.00 0.00 0.00 3.68
2745 2771 5.047660 ACAAACTGATAATTAGCCCGCAAAA 60.048 36.000 0.00 0.00 0.00 2.44
2746 2772 5.652994 AACTGATAATTAGCCCGCAAAAA 57.347 34.783 0.00 0.00 0.00 1.94
2747 2773 5.248870 ACTGATAATTAGCCCGCAAAAAG 57.751 39.130 0.00 0.00 0.00 2.27
2748 2774 4.947388 ACTGATAATTAGCCCGCAAAAAGA 59.053 37.500 0.00 0.00 0.00 2.52
2749 2775 5.066505 ACTGATAATTAGCCCGCAAAAAGAG 59.933 40.000 0.00 0.00 0.00 2.85
2750 2776 5.189928 TGATAATTAGCCCGCAAAAAGAGA 58.810 37.500 0.00 0.00 0.00 3.10
2751 2777 5.650266 TGATAATTAGCCCGCAAAAAGAGAA 59.350 36.000 0.00 0.00 0.00 2.87
2752 2778 4.864704 AATTAGCCCGCAAAAAGAGAAA 57.135 36.364 0.00 0.00 0.00 2.52
2753 2779 3.636282 TTAGCCCGCAAAAAGAGAAAC 57.364 42.857 0.00 0.00 0.00 2.78
2754 2780 1.692411 AGCCCGCAAAAAGAGAAACT 58.308 45.000 0.00 0.00 0.00 2.66
2755 2781 1.338020 AGCCCGCAAAAAGAGAAACTG 59.662 47.619 0.00 0.00 0.00 3.16
2756 2782 1.336755 GCCCGCAAAAAGAGAAACTGA 59.663 47.619 0.00 0.00 0.00 3.41
2757 2783 2.029918 GCCCGCAAAAAGAGAAACTGAT 60.030 45.455 0.00 0.00 0.00 2.90
2758 2784 3.190535 GCCCGCAAAAAGAGAAACTGATA 59.809 43.478 0.00 0.00 0.00 2.15
2759 2785 4.320935 GCCCGCAAAAAGAGAAACTGATAA 60.321 41.667 0.00 0.00 0.00 1.75
2760 2786 5.622233 GCCCGCAAAAAGAGAAACTGATAAT 60.622 40.000 0.00 0.00 0.00 1.28
2761 2787 6.389906 CCCGCAAAAAGAGAAACTGATAATT 58.610 36.000 0.00 0.00 0.00 1.40
2762 2788 7.535139 CCCGCAAAAAGAGAAACTGATAATTA 58.465 34.615 0.00 0.00 0.00 1.40
2763 2789 8.026607 CCCGCAAAAAGAGAAACTGATAATTAA 58.973 33.333 0.00 0.00 0.00 1.40
2764 2790 8.850452 CCGCAAAAAGAGAAACTGATAATTAAC 58.150 33.333 0.00 0.00 0.00 2.01
2765 2791 9.393249 CGCAAAAAGAGAAACTGATAATTAACA 57.607 29.630 0.00 0.00 0.00 2.41
2771 2797 9.574516 AAGAGAAACTGATAATTAACACAACCT 57.425 29.630 0.00 0.00 0.00 3.50
2772 2798 9.220767 AGAGAAACTGATAATTAACACAACCTC 57.779 33.333 0.00 0.00 0.00 3.85
2783 2809 3.708563 ACACAACCTCGTTCCAAAATG 57.291 42.857 0.00 0.00 0.00 2.32
2787 2813 5.125739 ACACAACCTCGTTCCAAAATGTAAA 59.874 36.000 0.00 0.00 0.00 2.01
2907 2933 1.956869 TCTCAGGCTCCTGGATTCAA 58.043 50.000 15.32 0.00 43.75 2.69
2965 2991 2.620115 CACAAAAGAAGAGCTGGAGCAA 59.380 45.455 0.00 0.00 45.16 3.91
3019 3045 4.607239 AGGAATTCAAGGATGTCATTGCT 58.393 39.130 7.93 0.00 37.53 3.91
3025 3051 2.753452 CAAGGATGTCATTGCTGAAGCT 59.247 45.455 3.61 0.00 42.66 3.74
3053 3079 6.423862 TCCGACAACGTAAGAAAGAAAAATG 58.576 36.000 0.00 0.00 43.62 2.32
3117 3143 3.680937 TGAAACTGTTTTCTTGACGACGT 59.319 39.130 7.28 0.00 41.64 4.34
3144 3170 4.400884 CAGGATGGGAGGATAGACTATTCG 59.599 50.000 0.00 0.00 0.00 3.34
3414 3445 0.255604 TGGTTGGCATCCGACATGAT 59.744 50.000 9.91 0.00 39.59 2.45
3422 3454 2.095869 GCATCCGACATGATGAGCAATC 60.096 50.000 0.00 0.00 43.94 2.67
3423 3455 2.245159 TCCGACATGATGAGCAATCC 57.755 50.000 0.00 0.00 34.00 3.01
3424 3456 1.202687 TCCGACATGATGAGCAATCCC 60.203 52.381 0.00 0.00 34.00 3.85
3425 3457 1.233019 CGACATGATGAGCAATCCCC 58.767 55.000 0.00 0.00 34.00 4.81
3426 3458 1.233019 GACATGATGAGCAATCCCCG 58.767 55.000 0.00 0.00 34.00 5.73
3427 3459 0.179009 ACATGATGAGCAATCCCCGG 60.179 55.000 0.00 0.00 34.00 5.73
3428 3460 0.109153 CATGATGAGCAATCCCCGGA 59.891 55.000 0.73 0.00 34.00 5.14
3429 3461 0.399454 ATGATGAGCAATCCCCGGAG 59.601 55.000 0.73 0.00 34.00 4.63
3430 3462 0.690744 TGATGAGCAATCCCCGGAGA 60.691 55.000 0.73 0.00 34.00 3.71
3431 3463 0.689623 GATGAGCAATCCCCGGAGAT 59.310 55.000 0.73 0.00 0.00 2.75
3437 3469 1.884235 CAATCCCCGGAGATTACTGC 58.116 55.000 11.27 0.00 34.69 4.40
3441 3473 0.830648 CCCCGGAGATTACTGCTTCA 59.169 55.000 0.73 0.00 32.26 3.02
3446 3478 2.286294 CGGAGATTACTGCTTCATGTGC 59.714 50.000 6.53 6.53 32.26 4.57
3452 3484 2.267174 ACTGCTTCATGTGCTTGAGT 57.733 45.000 12.86 6.93 0.00 3.41
3462 3494 3.492102 TGTGCTTGAGTAAGGAAGCTT 57.508 42.857 0.00 0.00 44.15 3.74
3540 3572 3.125658 GTGGCAAATTCAAATGGATGTGC 59.874 43.478 8.14 8.14 0.00 4.57
3641 3684 4.614555 TCAATCGGACATGTACAAATGC 57.385 40.909 9.21 0.00 0.00 3.56
3642 3685 4.006319 TCAATCGGACATGTACAAATGCA 58.994 39.130 9.21 0.00 0.00 3.96
3643 3686 4.457257 TCAATCGGACATGTACAAATGCAA 59.543 37.500 9.21 0.00 0.00 4.08
3644 3687 3.822594 TCGGACATGTACAAATGCAAC 57.177 42.857 9.21 0.00 0.00 4.17
3645 3688 2.158645 TCGGACATGTACAAATGCAACG 59.841 45.455 9.21 1.00 0.00 4.10
3646 3689 2.158645 CGGACATGTACAAATGCAACGA 59.841 45.455 9.21 0.00 0.00 3.85
3647 3690 3.488489 GGACATGTACAAATGCAACGAC 58.512 45.455 2.19 0.00 0.00 4.34
3648 3691 3.488489 GACATGTACAAATGCAACGACC 58.512 45.455 0.00 0.00 0.00 4.79
3649 3692 2.881513 ACATGTACAAATGCAACGACCA 59.118 40.909 0.00 0.00 0.00 4.02
3650 3693 3.058293 ACATGTACAAATGCAACGACCAG 60.058 43.478 0.00 0.00 0.00 4.00
3651 3694 1.876799 TGTACAAATGCAACGACCAGG 59.123 47.619 0.00 0.00 0.00 4.45
3746 3790 4.523813 CAATGTGTTTAAGACGTGTGTCC 58.476 43.478 0.00 0.00 46.74 4.02
3753 3798 6.018507 GTGTTTAAGACGTGTGTCCAAACTAT 60.019 38.462 17.06 0.00 46.74 2.12
3763 3808 7.227910 ACGTGTGTCCAAACTATAATCTGTTTT 59.772 33.333 0.00 0.00 34.60 2.43
3774 3819 6.708949 ACTATAATCTGTTTTCACCGTTGTGT 59.291 34.615 0.00 0.00 43.26 3.72
3775 3820 3.691049 ATCTGTTTTCACCGTTGTGTG 57.309 42.857 0.00 0.00 43.26 3.82
3776 3821 1.740585 TCTGTTTTCACCGTTGTGTGG 59.259 47.619 0.00 0.00 43.26 4.17
3777 3822 1.740585 CTGTTTTCACCGTTGTGTGGA 59.259 47.619 0.00 0.00 43.26 4.02
3778 3823 1.469308 TGTTTTCACCGTTGTGTGGAC 59.531 47.619 0.00 0.00 43.26 4.02
3779 3824 1.469308 GTTTTCACCGTTGTGTGGACA 59.531 47.619 0.00 0.00 43.26 4.02
3821 3874 4.153958 TCCAAATGTACACGTTGCAATC 57.846 40.909 0.59 0.00 0.00 2.67
3895 3948 2.946990 TCCGTTTTTCTCTCACAAACCC 59.053 45.455 0.00 0.00 0.00 4.11
3896 3949 2.286772 CCGTTTTTCTCTCACAAACCCG 60.287 50.000 0.00 0.00 0.00 5.28
4076 4132 7.448469 AGAGCAACTTGTAATAAAGATTGTGGT 59.552 33.333 0.00 0.00 0.00 4.16
4117 4173 4.813697 ACACAATGGCATGTTTTGGTTTAC 59.186 37.500 0.00 0.00 0.00 2.01
4149 4205 8.307483 ACTATATGATCAAGTAAGGTTCATCGG 58.693 37.037 0.00 0.00 0.00 4.18
4184 4240 2.489329 CGGATATGATGAATTGCACCCC 59.511 50.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.975616 ACAATGATGTTGCCACATAAGATAAAC 59.024 33.333 2.94 0.00 44.22 2.01
44 45 1.477558 GGGGGAGGTGCTACAATGATG 60.478 57.143 0.00 0.00 0.00 3.07
45 46 0.846693 GGGGGAGGTGCTACAATGAT 59.153 55.000 0.00 0.00 0.00 2.45
47 48 1.153168 CGGGGGAGGTGCTACAATG 60.153 63.158 0.00 0.00 0.00 2.82
48 49 1.615424 ACGGGGGAGGTGCTACAAT 60.615 57.895 0.00 0.00 0.00 2.71
65 66 1.926426 ATGGGCTAGGTTGGGCAGAC 61.926 60.000 0.00 0.00 0.00 3.51
69 70 1.060163 TCCTATGGGCTAGGTTGGGC 61.060 60.000 0.00 0.00 46.38 5.36
81 82 2.246719 GCACTAGTTGCCTCCTATGG 57.753 55.000 0.00 0.00 46.63 2.74
108 109 9.577110 TTTACGAACGAAAATGATGACTATAGT 57.423 29.630 4.68 4.68 0.00 2.12
118 119 5.877031 TGTGGTTTTTACGAACGAAAATGA 58.123 33.333 0.14 0.00 0.00 2.57
123 124 5.752472 TGTAGATGTGGTTTTTACGAACGAA 59.248 36.000 0.14 0.00 0.00 3.85
126 127 6.201425 TGAGTGTAGATGTGGTTTTTACGAAC 59.799 38.462 0.00 0.00 0.00 3.95
128 129 5.693104 GTGAGTGTAGATGTGGTTTTTACGA 59.307 40.000 0.00 0.00 0.00 3.43
130 131 6.854496 TGTGAGTGTAGATGTGGTTTTTAC 57.146 37.500 0.00 0.00 0.00 2.01
131 132 6.653320 GGATGTGAGTGTAGATGTGGTTTTTA 59.347 38.462 0.00 0.00 0.00 1.52
164 165 5.493870 CGTTAATAAACTACGACGTGTCACG 60.494 44.000 23.40 23.40 39.43 4.35
180 181 4.250464 CACCCACAAGAGCTCGTTAATAA 58.750 43.478 8.37 0.00 0.00 1.40
192 193 1.379916 CCCATGAGCACCCACAAGA 59.620 57.895 0.00 0.00 0.00 3.02
223 224 3.610911 TCTGCTCGACTCTGTTCATCTA 58.389 45.455 0.00 0.00 0.00 1.98
225 226 2.929531 TCTGCTCGACTCTGTTCATC 57.070 50.000 0.00 0.00 0.00 2.92
354 355 5.484715 GGTAATGAACCGCCTATATAAGCA 58.515 41.667 4.28 0.00 38.88 3.91
398 399 8.122472 ACACCTTATATTTTGAAAGGGAACAG 57.878 34.615 6.25 0.00 43.41 3.16
411 412 9.730420 GCACAAAAATCGATACACCTTATATTT 57.270 29.630 0.00 0.00 0.00 1.40
525 528 6.647212 TTTGTAGCGTTAGATTCATCACAG 57.353 37.500 0.00 0.00 0.00 3.66
526 529 7.609760 AATTTGTAGCGTTAGATTCATCACA 57.390 32.000 0.00 0.00 0.00 3.58
630 635 8.631480 ATTCTTGTTATTTACTCCTTCCGTTT 57.369 30.769 0.00 0.00 0.00 3.60
669 674 3.773119 AGCCGTCAGATCCCTTTTAACTA 59.227 43.478 0.00 0.00 0.00 2.24
670 675 2.572104 AGCCGTCAGATCCCTTTTAACT 59.428 45.455 0.00 0.00 0.00 2.24
674 679 0.984230 TGAGCCGTCAGATCCCTTTT 59.016 50.000 0.00 0.00 0.00 2.27
702 707 0.177604 CACATGGCTCCTCTCCTGAC 59.822 60.000 0.00 0.00 0.00 3.51
708 713 2.729479 CGGCTCACATGGCTCCTCT 61.729 63.158 0.00 0.00 0.00 3.69
735 740 1.670811 CCTCGCAATACCGCTTTGATT 59.329 47.619 0.00 0.00 0.00 2.57
752 757 6.341316 TCTTCAGTTATGTGTAGCATTCCTC 58.659 40.000 0.00 0.00 38.94 3.71
755 760 7.848051 CGAATTCTTCAGTTATGTGTAGCATTC 59.152 37.037 3.52 0.00 38.94 2.67
766 771 6.166279 TGAAGCTGTCGAATTCTTCAGTTAT 58.834 36.000 20.04 11.47 39.70 1.89
925 934 1.625870 CATGAAGAGTACGCACGCG 59.374 57.895 10.36 10.36 46.03 6.01
926 935 1.345176 GCATGAAGAGTACGCACGC 59.655 57.895 0.00 0.00 0.00 5.34
934 943 2.082231 GCACAGACATGCATGAAGAGT 58.918 47.619 32.75 20.27 45.39 3.24
948 957 1.986757 GAGGAGAGGCAGGCACAGA 60.987 63.158 0.00 0.00 0.00 3.41
1218 1233 4.082523 CGCACGTCCTCCATGGGT 62.083 66.667 13.02 0.00 36.20 4.51
1242 1257 1.215655 GCTCATCGCCGATGGTGTAC 61.216 60.000 25.40 8.31 40.15 2.90
1383 1398 1.300465 CATGATCTCCACCTCGCGG 60.300 63.158 6.13 0.00 0.00 6.46
1935 1950 0.620556 TCCTGACAAGATCCTTGGCC 59.379 55.000 9.77 0.00 0.00 5.36
1965 1980 2.217776 AGCCTATCCTTGGGGTTGATT 58.782 47.619 0.00 0.00 28.36 2.57
2043 2058 1.633171 CGTGCACGAAGCTAGCATC 59.367 57.895 34.93 14.15 45.94 3.91
2049 2064 2.588877 ACAAGCGTGCACGAAGCT 60.589 55.556 41.19 26.02 45.94 3.74
2065 2080 2.159476 TGCCTTCGTCATGTAGTACGAC 60.159 50.000 6.85 0.00 46.82 4.34
2067 2082 2.554806 TGCCTTCGTCATGTAGTACG 57.445 50.000 0.00 0.00 40.40 3.67
2071 2086 2.809446 TCGATTGCCTTCGTCATGTAG 58.191 47.619 5.45 0.00 40.03 2.74
2101 2118 7.203218 GTGGTCTGAAAAAGCTCAAGTTATTT 58.797 34.615 0.00 0.00 0.00 1.40
2102 2119 6.239036 GGTGGTCTGAAAAAGCTCAAGTTATT 60.239 38.462 0.00 0.00 0.00 1.40
2183 2200 1.620819 ACGAACTGCTTCATCCTGTCT 59.379 47.619 0.00 0.00 0.00 3.41
2259 2276 3.805207 AGTTACCTGAAGAAGCGTTGTT 58.195 40.909 0.00 0.00 0.00 2.83
2265 2282 9.438228 AAAGATTAGTTAGTTACCTGAAGAAGC 57.562 33.333 0.00 0.00 0.00 3.86
2459 2477 5.988310 TCCATCAGTTGCTGAATTTCATT 57.012 34.783 0.00 0.00 44.04 2.57
2712 2738 7.362574 GGCTAATTATCAGTTTGTTGGTGCTTA 60.363 37.037 0.00 0.00 0.00 3.09
2713 2739 6.389906 GCTAATTATCAGTTTGTTGGTGCTT 58.610 36.000 0.00 0.00 0.00 3.91
2737 2763 3.923017 ATCAGTTTCTCTTTTTGCGGG 57.077 42.857 0.00 0.00 0.00 6.13
2738 2764 8.850452 GTTAATTATCAGTTTCTCTTTTTGCGG 58.150 33.333 0.00 0.00 0.00 5.69
2739 2765 9.393249 TGTTAATTATCAGTTTCTCTTTTTGCG 57.607 29.630 0.00 0.00 0.00 4.85
2745 2771 9.574516 AGGTTGTGTTAATTATCAGTTTCTCTT 57.425 29.630 0.00 0.00 0.00 2.85
2746 2772 9.220767 GAGGTTGTGTTAATTATCAGTTTCTCT 57.779 33.333 0.00 0.00 0.00 3.10
2747 2773 8.169268 CGAGGTTGTGTTAATTATCAGTTTCTC 58.831 37.037 0.00 3.00 0.00 2.87
2748 2774 7.660208 ACGAGGTTGTGTTAATTATCAGTTTCT 59.340 33.333 0.00 0.00 0.00 2.52
2749 2775 7.803724 ACGAGGTTGTGTTAATTATCAGTTTC 58.196 34.615 0.00 0.00 0.00 2.78
2750 2776 7.739498 ACGAGGTTGTGTTAATTATCAGTTT 57.261 32.000 0.00 0.00 0.00 2.66
2751 2777 7.094933 GGAACGAGGTTGTGTTAATTATCAGTT 60.095 37.037 0.00 0.00 0.00 3.16
2752 2778 6.370718 GGAACGAGGTTGTGTTAATTATCAGT 59.629 38.462 0.00 0.00 0.00 3.41
2753 2779 6.370442 TGGAACGAGGTTGTGTTAATTATCAG 59.630 38.462 0.00 0.00 0.00 2.90
2754 2780 6.231951 TGGAACGAGGTTGTGTTAATTATCA 58.768 36.000 0.00 0.00 0.00 2.15
2755 2781 6.730960 TGGAACGAGGTTGTGTTAATTATC 57.269 37.500 0.00 0.00 0.00 1.75
2756 2782 7.513371 TTTGGAACGAGGTTGTGTTAATTAT 57.487 32.000 0.00 0.00 0.00 1.28
2757 2783 6.939132 TTTGGAACGAGGTTGTGTTAATTA 57.061 33.333 0.00 0.00 0.00 1.40
2758 2784 5.838531 TTTGGAACGAGGTTGTGTTAATT 57.161 34.783 0.00 0.00 0.00 1.40
2759 2785 5.838531 TTTTGGAACGAGGTTGTGTTAAT 57.161 34.783 0.00 0.00 0.00 1.40
2760 2786 5.125739 ACATTTTGGAACGAGGTTGTGTTAA 59.874 36.000 0.00 0.00 0.00 2.01
2761 2787 4.641094 ACATTTTGGAACGAGGTTGTGTTA 59.359 37.500 0.00 0.00 0.00 2.41
2762 2788 3.445805 ACATTTTGGAACGAGGTTGTGTT 59.554 39.130 0.00 0.00 0.00 3.32
2763 2789 3.020984 ACATTTTGGAACGAGGTTGTGT 58.979 40.909 0.00 0.00 0.00 3.72
2764 2790 3.708563 ACATTTTGGAACGAGGTTGTG 57.291 42.857 0.00 0.00 0.00 3.33
2765 2791 5.838531 TTTACATTTTGGAACGAGGTTGT 57.161 34.783 0.00 0.00 0.00 3.32
2766 2792 5.172411 CGTTTTACATTTTGGAACGAGGTTG 59.828 40.000 1.11 0.00 44.01 3.77
2767 2793 5.163632 ACGTTTTACATTTTGGAACGAGGTT 60.164 36.000 12.98 0.00 44.01 3.50
2768 2794 4.336153 ACGTTTTACATTTTGGAACGAGGT 59.664 37.500 12.98 0.00 44.01 3.85
2769 2795 4.851010 ACGTTTTACATTTTGGAACGAGG 58.149 39.130 12.98 0.00 44.01 4.63
2770 2796 6.799786 AAACGTTTTACATTTTGGAACGAG 57.200 33.333 7.96 0.00 44.01 4.18
2771 2797 6.979509 CAAAACGTTTTACATTTTGGAACGA 58.020 32.000 24.79 0.00 44.01 3.85
2783 2809 5.959652 ATTGAACAGCCAAAACGTTTTAC 57.040 34.783 24.79 19.19 0.00 2.01
2787 2813 6.592220 AGTTTAAATTGAACAGCCAAAACGTT 59.408 30.769 0.00 0.00 0.00 3.99
2856 2882 7.938140 TCTCTGTTTCTTTTCTTTTTCCAGA 57.062 32.000 0.00 0.00 0.00 3.86
2907 2933 6.521527 AGGTATATGAGCCTCCAAAAATCT 57.478 37.500 0.00 0.00 0.00 2.40
2965 2991 3.181450 ACAACTTCTGCTCTTGTAAGGCT 60.181 43.478 6.63 0.00 0.00 4.58
3019 3045 1.270094 ACGTTGTCGGAATCAGCTTCA 60.270 47.619 0.00 0.00 41.85 3.02
3025 3051 4.873817 TCTTTCTTACGTTGTCGGAATCA 58.126 39.130 0.00 0.00 39.28 2.57
3066 3092 6.929049 CCTTTCGATGCATTTACCATCTACTA 59.071 38.462 0.00 0.00 37.52 1.82
3067 3093 5.760253 CCTTTCGATGCATTTACCATCTACT 59.240 40.000 0.00 0.00 37.52 2.57
3068 3094 5.758296 TCCTTTCGATGCATTTACCATCTAC 59.242 40.000 0.00 0.00 37.52 2.59
3117 3143 3.078153 AGTCTATCCTCCCATCCTGCATA 59.922 47.826 0.00 0.00 0.00 3.14
3144 3170 0.179111 TCATCATCGCCACGAACTCC 60.179 55.000 0.00 0.00 39.99 3.85
3414 3445 1.416401 GTAATCTCCGGGGATTGCTCA 59.584 52.381 35.18 16.01 36.69 4.26
3422 3454 0.830648 TGAAGCAGTAATCTCCGGGG 59.169 55.000 0.00 0.00 0.00 5.73
3423 3455 2.158900 ACATGAAGCAGTAATCTCCGGG 60.159 50.000 0.00 0.00 0.00 5.73
3424 3456 2.868583 CACATGAAGCAGTAATCTCCGG 59.131 50.000 0.00 0.00 0.00 5.14
3425 3457 2.286294 GCACATGAAGCAGTAATCTCCG 59.714 50.000 0.00 0.00 0.00 4.63
3426 3458 3.539604 AGCACATGAAGCAGTAATCTCC 58.460 45.455 15.23 0.00 0.00 3.71
3427 3459 4.633126 TCAAGCACATGAAGCAGTAATCTC 59.367 41.667 15.23 0.00 0.00 2.75
3428 3460 4.582869 TCAAGCACATGAAGCAGTAATCT 58.417 39.130 15.23 0.00 0.00 2.40
3429 3461 4.394300 ACTCAAGCACATGAAGCAGTAATC 59.606 41.667 15.23 0.00 0.00 1.75
3430 3462 4.330250 ACTCAAGCACATGAAGCAGTAAT 58.670 39.130 15.23 0.00 0.00 1.89
3431 3463 3.743521 ACTCAAGCACATGAAGCAGTAA 58.256 40.909 15.23 0.49 0.00 2.24
3437 3469 4.142730 GCTTCCTTACTCAAGCACATGAAG 60.143 45.833 0.00 0.00 43.87 3.02
3441 3473 3.710209 AGCTTCCTTACTCAAGCACAT 57.290 42.857 6.44 0.00 46.37 3.21
3446 3478 7.327214 ACTATTCAGAAGCTTCCTTACTCAAG 58.673 38.462 22.81 12.17 0.00 3.02
3452 3484 6.620877 TTGGACTATTCAGAAGCTTCCTTA 57.379 37.500 22.81 8.54 0.00 2.69
3462 3494 7.201794 CGTAGTGGTAGATTTGGACTATTCAGA 60.202 40.741 0.00 0.00 0.00 3.27
3499 3531 3.369681 CCACCACTTTACCTACGGCATAA 60.370 47.826 0.00 0.00 0.00 1.90
3500 3532 2.168936 CCACCACTTTACCTACGGCATA 59.831 50.000 0.00 0.00 0.00 3.14
3501 3533 1.065709 CCACCACTTTACCTACGGCAT 60.066 52.381 0.00 0.00 0.00 4.40
3562 3594 2.508891 CGGATGCGCTCGAGTGAAC 61.509 63.158 29.41 17.33 0.00 3.18
3574 3606 0.383949 GAGAGGAGACAGTCGGATGC 59.616 60.000 0.00 0.00 0.00 3.91
3641 3684 0.179156 GCATGCATTCCTGGTCGTTG 60.179 55.000 14.21 0.00 0.00 4.10
3642 3685 0.608856 TGCATGCATTCCTGGTCGTT 60.609 50.000 18.46 0.00 0.00 3.85
3643 3686 1.002257 TGCATGCATTCCTGGTCGT 60.002 52.632 18.46 0.00 0.00 4.34
3644 3687 1.307355 TGTGCATGCATTCCTGGTCG 61.307 55.000 25.64 0.00 0.00 4.79
3645 3688 0.171903 GTGTGCATGCATTCCTGGTC 59.828 55.000 25.64 8.75 0.00 4.02
3646 3689 0.540133 TGTGTGCATGCATTCCTGGT 60.540 50.000 25.64 0.00 0.00 4.00
3647 3690 0.821517 ATGTGTGCATGCATTCCTGG 59.178 50.000 25.64 0.00 33.37 4.45
3648 3691 1.202371 GGATGTGTGCATGCATTCCTG 60.202 52.381 25.64 0.00 42.14 3.86
3649 3692 1.108776 GGATGTGTGCATGCATTCCT 58.891 50.000 25.64 12.56 42.14 3.36
3650 3693 0.818938 TGGATGTGTGCATGCATTCC 59.181 50.000 25.64 24.56 46.20 3.01
3719 3762 5.790003 CACACGTCTTAAACACATTGCATAG 59.210 40.000 0.00 0.00 0.00 2.23
3746 3790 8.073768 ACAACGGTGAAAACAGATTATAGTTTG 58.926 33.333 7.88 0.00 37.94 2.93
3774 3819 2.548057 GCTTTGAAGATCGTGTTGTCCA 59.452 45.455 0.00 0.00 0.00 4.02
3775 3820 2.808543 AGCTTTGAAGATCGTGTTGTCC 59.191 45.455 0.00 0.00 0.00 4.02
3776 3821 4.923871 TCTAGCTTTGAAGATCGTGTTGTC 59.076 41.667 0.00 0.00 0.00 3.18
3777 3822 4.883083 TCTAGCTTTGAAGATCGTGTTGT 58.117 39.130 0.00 0.00 0.00 3.32
3778 3823 5.006165 GGATCTAGCTTTGAAGATCGTGTTG 59.994 44.000 15.00 0.00 46.01 3.33
3779 3824 5.112686 GGATCTAGCTTTGAAGATCGTGTT 58.887 41.667 15.00 0.00 46.01 3.32
3783 3831 6.259608 ACATTTGGATCTAGCTTTGAAGATCG 59.740 38.462 15.00 6.40 46.01 3.69
3821 3874 6.991485 ATAAGTTGCTTCGTGAAAACATTG 57.009 33.333 1.37 0.00 0.00 2.82
4004 4058 2.624169 TGCCGGTGCAAACTCTTAC 58.376 52.632 1.90 0.00 46.66 2.34
4023 4077 7.461107 TGTCACACTAGTTTTCTTTTCGAAAG 58.539 34.615 10.98 5.92 42.22 2.62
4076 4132 3.081061 GTGTACACTGGGATTGATTGCA 58.919 45.455 18.92 0.00 0.00 4.08
4117 4173 8.964476 ACCTTACTTGATCATATAGTGTTTGG 57.036 34.615 8.50 7.47 0.00 3.28
4122 4178 9.133627 CGATGAACCTTACTTGATCATATAGTG 57.866 37.037 8.50 0.00 31.24 2.74
4149 4205 0.035820 TATCCGCCACCACCTGTTTC 60.036 55.000 0.00 0.00 0.00 2.78


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.